how will I get to know that the system have shrunken enough, and which file I need to solvate.
On Thu, Oct 2, 2014 at 9:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/2/14 8:50 AM, Anurag Dobhal wrote: > >> Thanks Justin >> >> I m running the command >> >> " mdrun -s em.tpr " and I did get the confout.gro file as output. >> >> after that I am running the command >> >> " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 >> area_shrink1.dat " >> and then again the energy minimization command. >> >> " mdrun -s em.tpr" >> >> After that I am solvating the system. >> I did put a local copy of vdwradii.dat in my working directorie and >> change >> the value of C from 0.15 to 0.375. >> >> >> I am solvating my system by the command >> >> " genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p >> topol.top " >> >> after that I am adding the ions in the system by the command >> >> " grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr" >> >> But now I am getting an error >> >> number of coordinates in coordinate file (system_solv.gro, 8218) >> does not match topology (topol.top, 1956) >> >> >> can you please help what caused this error. >> >> > Don't solvate the intermediate steps. It makes no physical sense. Only > solvate when you have shrunk the system to an appropriate size based on > APL. Regardless, the number of atoms in the system is way too small to be > correct for the tutorial system. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.